X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=c11e1ecee6b18adcc25a1f55878a8262f8cde1b6;hb=91c5d2144a780716e755e99882acffe46b40f18f;hp=12f252d69106e6cc70d73092b0adc162f90f2007;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 12f252d..c11e1ec 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -21,48 +21,101 @@ package jalview.schemes;
 import java.awt.*;
 
 
-public class ScoreColourScheme extends ResidueColourScheme {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ScoreColourScheme extends ResidueColourScheme
+{
+    /** DOCUMENT ME!! */
     public double min;
+
+    /** DOCUMENT ME!! */
     public double max;
+
+    /** DOCUMENT ME!! */
     public double[] scores;
 
-    public ScoreColourScheme(double[] scores, double min, double max) {
+    /**
+     * Creates a new ScoreColourScheme object.
+     *
+     * @param scores DOCUMENT ME!
+     * @param min DOCUMENT ME!
+     * @param max DOCUMENT ME!
+     */
+    public ScoreColourScheme(double[] scores, double min, double max)
+    {
         super();
 
         this.scores = scores;
         this.min = min;
         this.max = max;
-    }
-
-    public Color findColour(String s, int j) {
-        if (threshold > 0) {
-            if (!aboveThreshold(s, j)) {
-                return Color.white;
-            }
-        }
 
-        float red = (float) (scores[((Integer) ResidueProperties.aaHash.get(s)).intValue()] -
-            (float) min) / (float) (max - min);
+        // Make colours in constructor
+        // Why wasn't this done earlier?
+        int i, iSize=scores.length;
+        colors = new Color[scores.length];
+        for (i = 0; i < iSize; i++)
+        {
+          float red = (float) (scores[i] - (float) min) / (float) (max - min);
 
-        if (red > 1.0f) {
+          if (red > 1.0f)
+          {
             red = 1.0f;
-        }
+          }
 
-        if (red < 0.0f) {
+          if (red < 0.0f)
+          {
             red = 0.0f;
+          }
+          colors[i] = makeColour(red);
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String s, int j)
+    {
+        if (threshold > 0)
+        {
+            if (!aboveThreshold(s, j))
+            {
+                return Color.white;
+            }
         }
 
         char c = s.charAt(0);
 
-        if (jalview.util.Comparison.isGap((c))) {
+        if (jalview.util.Comparison.isGap((c)))
+        {
             return Color.white;
         }
 
-        // This isn';t great - pool of colours in here?
-        return makeColour(red);
+        currentColour = colors[((Integer) ResidueProperties.aaHash.get(s)).intValue()];
+
+        if(conservationColouring)
+         applyConservation(j);
+
+        return currentColour;
     }
 
-    public Color makeColour(float c) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color makeColour(float c)
+    {
         return new Color(c, (float) 0.0, (float) 1.0 - c);
     }
 }